To investigate the association between plasma homocysteine levels and glaucomatous retinal nerve fiber layer (RNFL) defect in South Korean population. This retrospective cross-sectional study included subjects who underwent screening at Kangbuk Samsung Hospital Health Screening Center between August 2012 and July 2013. Subjects underwent physical examination and provided samples for laboratory analysis of homocysteine. Subjects were divided equally into four quartiles (Qs) based on plasma homocysteine level. Digital fundus photographs of both eyes were obtained. Determination of glaucomatous disc appearance was based on criteria set forth by the International Society of Geographical and Epidemiological Ophthalmology and based on the appearance of the RNFL and optic disc. Multivariate logistic regression models were used to define elevated glaucoma risk with P < 0.2 on univariate analysis. A total of 78,049 subjects were included; 76,093 subjects were male, and 1956 subjects were female. When analyzed by gender, the mean homocysteine level in the male group with glaucomatous RNFL defects (11.05 ± 3.80 µmol/L) was higher than those without RNFL defects (10.81 ± 4.12 µmol/L (P = 0.000, χ2 test). Upon multifactorial logistic regression analysis adjusted for age, gender, creatinine, diabetes mellitus, hypertension, and hyperlipidemia, glaucomatous RNFL defects had a significant correlation with plasma homocysteine level. Based on the Q2 level, the odds ratio (OR) of Q3 was 1.267, while the OR of Q4 was 1.285 (95% CI = 1.067-1.505, 1.081-1.529, respectively, P for trend = 0.001). Our results suggest that homocysteine level is associated with the presence of glaucomatous RNFL defects.